Laboratory of Comparative Ethology and Biocommunication, Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia.
Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.
J Exp Zool B Mol Dev Evol. 2024 Jun;342(4):368-379. doi: 10.1002/jez.b.23244. Epub 2024 Feb 26.
Hybrid parthenogenetic animals are an exceptionally interesting model for studying the mechanisms and evolution of sexual and asexual reproduction. A diploid parthenogenetic lizard Darevskia unisexualis is a result of an ancestral cross between a maternal species Darevskia raddei nairensis and a paternal species Darevskia valentini and presents a unique opportunity for a cytogenetic and computational analysis of a hybrid karyotype. Our previous results demonstrated a significant divergence between the pericentromeric DNA sequences of the parental Darevskia species; however, an in-depth comparative study of their pericentromeres is still lacking. Here, using target sequencing of microdissected pericentromeric regions, we reveal and compare the repertoires of the pericentromeric tandem repeats of the parental Darevskia lizards. We found species-specific sequences of the major pericentromeric tandem repeat CLsat, which allowed computational prediction and experimental validation of fluorescent DNA probes discriminating parental chromosomes within the hybrid karyotype of D. unisexualis. Moreover, we have implemented a generalizable computational method, based on the optimization of the Levenshtein distance between tandem repeat monomers, for finding species-specific fluorescent probes for pericentromere staining. In total, we anticipate that our comparative analysis of Darevskia pericentromeric repeats, the species-specific fluorescent probes that we found and the pipeline that we developed will form a basis for the future detailed cytogenomic studies of a wide range of natural and laboratory hybrids.
杂种孤雌生殖动物是研究有性和无性繁殖的机制和进化的一个非常有趣的模型。一种二倍体孤雌生殖蜥蜴 Darevskia unisexualis 是母体物种 Darevskia raddei nairensis 和父体物种 Darevskia valentini 之间的祖先杂交的结果，为杂种染色体组的细胞遗传学和计算分析提供了独特的机会。我们之前的研究结果表明，亲代 Darevskia 物种的着丝粒周围 DNA 序列存在显著差异；然而，对它们的着丝粒周围区进行深入的比较研究仍然缺乏。在这里，我们使用微切割着丝粒区域的靶向测序，揭示并比较了亲代 Darevskia 蜥蜴的着丝粒串联重复序列库。我们发现了主要着丝粒串联重复 CLsat 的种特异性序列，这使得能够对 D. unisexualis 的杂种染色体组内的亲本染色体进行荧光 DNA 探针的计算预测和实验验证。此外，我们还实施了一种可推广的计算方法，该方法基于串联重复单体之间的 Levenshtein 距离的优化，用于寻找种特异性的荧光探针，以用于着丝粒染色。总的来说，我们预计我们对 Darevskia 着丝粒重复序列的比较分析、我们发现的种特异性荧光探针以及我们开发的管道将为未来对广泛的自然和实验室杂种的详细细胞基因组学研究奠定基础。
